Developers - API
Internal configuration system
A Python module to maintain unique, run-wide aslprep settings.
This module implements the memory structures to keep a consistent, singleton config.
Settings are passed across processes via filesystem, and a copy of the settings for
each run and subject is left under
<aslprep_dir>/sub-<participant_id>/log/<run_unique_id>/aslprep.toml
.
Settings are stored using ToML.
The module has a to_filename()
function to allow writing out
the settings to hard disk in ToML format, which looks like:
This config file is used to pass the settings across processes,
using the load()
function.
Configuration sections
- class environment[source]
Read-only options regarding the platform and environment.
Crawls runtime descriptive settings (e.g., default FreeSurfer license, execution environment, nipype and ASLPrep versions, etc.). The
environment
section is not loaded in from file, only written out when settings are exported. This config section is useful when reporting issues, and these variables are tracked whenever the user does not opt-out using the--notrack
argument.- cpu_count = 2
Number of available CPUs.
- exec_docker_version = None
Version of Docker Engine.
- exec_env = 'posix'
A string representing the execution platform.
- free_mem = 6.2
Free memory at start.
- nipype_version = '1.8.6'
Nipype’s current version.
- overcommit_limit = '50%'
Linux’s kernel virtual memory overcommit limits.
- overcommit_policy = 'heuristic'
Linux’s kernel virtual memory overcommit policy.
- templateflow_version = '23.1.0'
The TemplateFlow client version installed.
- version = '0.6.0'
ASLPrep’s version.
- class execution[source]
Configure run-level settings.
- aslprep_dir = None
Root of ASLPrep BIDS Derivatives dataset.
- bids_database_dir = None
Path to the directory containing SQLite database indices for the input BIDS dataset.
- bids_description_hash = None
Checksum (SHA256) of the
dataset_description.json
of the BIDS dataset.
- bids_dir = None
An existing path to the dataset, which must be BIDS-compliant.
- bids_filters = None
A dictionary of BIDS selection filters.
- boilerplate_only = False
Only generate a boilerplate.
- debug = []
Debug mode(s).
- derivatives = []
Path(s) to search for pre-computed derivatives
- fs_license_file = None
An existing file containing a FreeSurfer license.
- fs_subjects_dir = None
FreeSurfer’s subjects directory.
- layout = None
A
BIDSLayout
object, seeinit()
.
- log_dir = None
The path to a directory that contains execution logs.
- log_level = 25
Output verbosity.
- low_mem = None
Utilize uncompressed NIfTIs and other tricks to minimize memory allocation.
- md_only_boilerplate = False
Do not convert boilerplate from MarkDown to LaTex and HTML.
- notrack = False
Do not collect telemetry information for ASLPrep.
- output_dir = None
Folder where derivatives will be stored.
- output_spaces = None
List of (non)standard spaces designated (with the
--output-spaces
flag of the command line) as spatial references for outputs.
- participant_label = None
List of participant identifiers that are to be preprocessed.
- reports_only = False
Only build the reports, based on the reportlets found in a cached working directory.
- run_uuid = '20231209-202910_70210aa2-5b95-445a-835c-e0101719c16a'
Unique identifier of this particular run.
- sloppy = False
Run in sloppy mode (meaning, suboptimal parameters that minimize run-time).
- task_id = None
Select a particular task from all available in the dataset.
- templateflow_home = PosixPath('/home/docs/.cache/templateflow')[source]
The root folder of the TemplateFlow client.
- work_dir = PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/aslprep/checkouts/0.6.0/docs/work')[source]
Path to a working directory where intermediate results will be available.
- write_graph = False
Write out the computational graph corresponding to the planned preprocessing.
- class workflow[source]
Configure the particular execution graph of this workflow.
- anat_only = False
Execute the anatomical preprocessing only.
- asl2t1w_dof = None
Degrees of freedom of the ASL-to-T1w registration steps.
- asl2t1w_init = 'register'
Whether to use standard coregistration (‘register’) or to initialize coregistration from the ASL image-header (‘header’).
- basil = False
Run BASIL, FSL utils to compute CBF with spatial regularization and partial volume correction.
- cifti_output = None
Generate HCP Grayordinates, accepts either
'91k'
(default) or'170k'
.
- dummy_scans = 0
Number of label-control volume pairs to delete before CBF computation.
- fmap_bspline = None
Regularize fieldmaps with a field of B-Spline basis.
- fmap_demean = None
Remove the mean from fieldmaps.
- force_syn = None
Run fieldmap-less susceptibility-derived distortions estimation.
- hires = None
Run FreeSurfer
recon-all
with the-hires
flag.
- ignore = None
Ignore particular steps for ASLPrep.
- level = 'full'
Level of preprocessing to complete. One of [‘minimal’, ‘resampling’, ‘full’].
- longitudinal = False
Run FreeSurfer
recon-all
with the--longitudinal
flag.
- m0_scale = 1.0
Relative scale between ASL (delta-M) and M0.
- medial_surface_nan = None
Fill medial surface with NaNs when sampling.
- project_goodvoxels = False
Exclude voxels with locally high coefficient of variation from sampling.
- run_msmsulc = True
Run Multimodal Surface Matching surface registration.
- run_reconall = True
Run FreeSurfer’s surface reconstruction.
- scorescrub = False
Run SCORE/SCRUB, Sudipto Dolui’s algorithms for denoising CBF.
- skull_strip_fixed_seed = False
Fix a seed for skull-stripping.
- skull_strip_t1w = 'force'
Skip brain extraction of the T1w image (default is
force
, meaning that ASLPrep will run brain extraction of the T1w).
- skull_strip_template = 'OASIS30ANTs'
Change default brain extraction template.
- smooth_kernel = 5.0
Kernel size for smoothing M0.
- spaces = None
Keeps the
SpatialReferences
instance keeping standard and nonstandard spaces.
- use_bbr = None
Run boundary-based registration for ASL-to-T1w registration.
- use_ge = None
Run GE-specific processing. False means don’t, True means do, None means determine automatically.
- use_syn_sdc = None
Run fieldmap-less susceptibility-derived distortions estimation in the absence of any alternatives.
- class nipype[source]
Nipype settings.
- crashfile_format = 'txt'
The file format for crashfiles, either text or pickle.
- get_linked_libs = False
Run NiPype’s tool to enlist linked libraries for every interface.
- memory_gb = None
Estimation in GB of the RAM this workflow can allocate at any given time.
- nprocs = 2
Number of processes (compute tasks) that can be run in parallel (multiprocessing only).
- omp_nthreads = None
Number of CPUs a single process can access for multithreaded execution.
- plugin = 'MultiProc'
NiPype’s execution plugin.
- plugin_args = {'maxtasksperchild': 1, 'raise_insufficient': False}
Settings for NiPype’s execution plugin.
- resource_monitor = False
Enable resource monitor.
- stop_on_first_crash = True
Whether the workflow should stop or continue after the first error.
Usage
A config file is used to pass settings and collect information as the execution graph is built across processes.
from aslprep import config
config_file = config.execution.work_dir / '.aslprep.toml'
config.to_filename(config_file)
# Call build_workflow(config_file, retval) in a subprocess
with Manager() as mgr:
from aslprep.cli.workflow import build_workflow
retval = mgr.dict()
p = Process(target=build_workflow, args=(str(config_file), retval))
p.start()
p.join()
config.load(config_file)
# Access configs from any code section as:
value = config.section.setting
Logging
Other responsibilities
The config
is responsible for other conveniency actions.
Switching Python’s
multiprocessing
to forkserver mode.Set up a filter for warnings as early as possible.
Automated I/O magic operations. Some conversions need to happen in the store/load processes (e.g., from/to
Path
<->str
,BIDSLayout
, etc.)
- load(filename, skip=None, init=True)[source]
Load settings from file.
- Parameters:
filename (
os.PathLike
) – TOML file containing ASLPrep configuration.skip (dict or None) – Sets of values to ignore during load, keyed by section name
init (bool or
Container
) – Initialize all, none, or a subset of configurations.
aslprep.workflows
: Workflows
ASLprep base processing workflows. |
|
Workflows to apply changes to ASL data. |
|
Preprocessing workflows for ASL data. |
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Workflows for calculating CBF. |
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Workflows for calculating confounds for ASL data. |
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Fit workflows for ASLPrep. |
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Workflows for estimating and correcting head motion in ASL images. |
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Workflows for writing out derivative files. |
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Workflows for plotting ASLPrep derivatives. |
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Workflows for generating reference images. |
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Utility workflows. |
aslprep.interfaces
: Interfaces
Nipype interfaces for aslprep.
ANTS interfaces. |
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Adapted interfaces from Niworkflows. |
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Interfaces for calculating CBF. |
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Interfaces for calculating and collecting confounds. |
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Handling functional connectvity. |
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Plotting interfaces. |
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Interfaces for building reference images. |
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Interfaces to generate reportlets. |
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Utility interfaces for ASLPrep. |
aslprep.utils
: Utilities
Utility functions for aslprep.
Functions for working with ASL data. |
|
Functions for working with atlases. |
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Utilities to handle BIDS inputs. |
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Functions for calculating CBF. |
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Functions for calculating and collecting confounds. |
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Miscellaneous utilities. |
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Plotting functions and classes. |
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Stripped out routines for Sentry. |
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Utilities for tracking and filtering spaces. |
aslprep.data
: Data resources
ASLPrep data files
- load(*segments) Path [source]
Load package files relative to
aslprep.data
.This package contains the following (top-level) files/directories:
NOTICE
aslprep_bids_config.json
atlases/
boilerplate.bib
io_spec.json
paper_sample.yml
reports-spec.yml
- load.readable(*segments) Traversable [source]
Provide read access to a resource through a Path-like interface.
This file may or may not exist on the filesystem, and may be efficiently used for read operations, including directory traversal.
This result is not cached or copied to the filesystem in cases where that would be necessary.
- load.as_path(*segments) AbstractContextManager[Path] [source]
Ensure data is available as a
Path
.This method generates a context manager that yields a Path when entered.
This result is not cached, and any temporary files that are created are deleted when the context is exited.
- load.cached(*segments) Path [source]
Ensure data is available as a
Path
.Any temporary files that are created remain available throughout the duration of the program, and are deleted when Python exits.
Results are cached so that multiple calls do not unpack the same data multiple times, but the cache is sensitive to the specific argument(s) passed.
- class Loader(anchor: str | module)[source]
A loader for package files relative to a module
This class wraps
importlib.resources
to provide a getter function with an interpreter-lifetime scope. For typical packages it simply passes through filesystem paths asPath
objects. For zipped distributions, it will unpack the files into a temporary directory that is cleaned up on interpreter exit.This loader accepts a fully-qualified module name or a module object.
Expected usage:
'''Data package .. autofunction:: load_data .. automethod:: load_data.readable .. automethod:: load_data.as_path .. automethod:: load_data.cached ''' from fmriprep.data import Loader load_data = Loader(__package__)
Loader
objects implement thecallable()
interface and generate a docstring, and are intended to be treated and documented as functions.For greater flexibility and improved readability over the
importlib.resources
interface, explicit methods are provided to access resources.On-filesystem
Lifetime
Method
True
Interpreter
True
with context
False
n/a
It is also possible to use
Loader
directly:from fmriprep.data import Loader Loader(other_package).readable('data/resource.ext').read_text() with Loader(other_package).as_path('data') as pkgdata: # Call function that requires full Path implementation func(pkgdata) # contrast to from importlib_resources import files, as_file files(other_package).joinpath('data/resource.ext').read_text() with as_file(files(other_package) / 'data') as pkgdata: func(pkgdata)
- readable(*segments) Traversable [source]
Provide read access to a resource through a Path-like interface.
This file may or may not exist on the filesystem, and may be efficiently used for read operations, including directory traversal.
This result is not cached or copied to the filesystem in cases where that would be necessary.
- as_path(*segments) AbstractContextManager[Path] [source]
Ensure data is available as a
Path
.This method generates a context manager that yields a Path when entered.
This result is not cached, and any temporary files that are created are deleted when the context is exited.
- cached(*segments) Path [source]
Ensure data is available as a
Path
.Any temporary files that are created remain available throughout the duration of the program, and are deleted when Python exits.
Results are cached so that multiple calls do not unpack the same data multiple times, but the cache is sensitive to the specific argument(s) passed.
ASLPrep data files |